Magnesium in PDB 5jvh: The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin

The structure of The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin, PDB code: 5jvh was solved by A.Yonath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.85 / 3.58
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	169.475, 407.380, 692.552, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 24.7

The structure of The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 120; Page 13, Binding sites: 121 - 123;

Binding sites:

The binding sites of Magnesium atom in the The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin (pdb code 5jvh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 123 binding sites of Magnesium where determined in the The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin, PDB code: 5jvh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 123 in the The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2902 b:32.7 occ:1.00 O6 X:G2699 3.6 32.7 1.0 O6 X:G2698 3.9 32.9 1.0 N7 X:G2698 4.2 33.7 1.0 O6 X:G2697 4.4 33.2 1.0 N7 X:G2697 4.5 33.8 1.0 O4 X:U2693 4.5 31.5 1.0 C6 X:G2699 4.6 32.8 1.0 C6 X:G2698 4.7 33.2 1.0 C5 X:G2698 4.9 33.5 1.0 C6 X:G2697 4.9 33.6 1.0 C5 X:G2697 4.9 33.8 1.0

Magnesium binding site 2 out of 123 in the The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2903 b:37.7 occ:1.00 OP2 X:C583 2.1 48.9 1.0 P X:C583 3.6 48.7 1.0 OP2 X:U585 3.8 37.9 1.0 O4 X:U585 3.8 40.8 1.0 O6 X:G586 3.8 49.1 1.0 C5 X:U585 3.9 40.0 1.0 C4 X:U585 4.2 40.6 1.0 O5' X:C583 4.2 48.1 1.0 C5' X:G582 4.4 61.0 1.0 OP1 X:C583 4.4 48.5 1.0 O5' X:G582 4.5 61.2 1.0 N6 X:A587 4.5 39.1 1.0 C4' X:G582 4.7 60.6 1.0 O3' X:G582 4.7 59.3 1.0 C3' X:G582 4.7 60.0 1.0 O6 X:G572 4.8 42.4 1.0 N4 X:C573 4.9 45.2 1.0 C6 X:G586 4.9 49.3 1.0 N7 X:G586 5.0 48.4 1.0 C6 X:U585 5.0 39.8 1.0

Magnesium binding site 3 out of 123 in the The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2904 b:32.8 occ:1.00 O6 X:G1993 3.8 32.5 1.0 O6 X:G1992 3.8 32.4 1.0 N7 X:G1992 4.1 33.1 1.0 N7 X:G1993 4.2 33.4 1.0 C6 X:G1992 4.4 32.7 1.0 O4 X:U1994 4.5 33.1 1.0 C5 X:G1992 4.5 33.1 1.0 OP2 X:U1280 4.5 33.7 1.0 C6 X:G1993 4.7 32.8 1.0 C5 X:G1993 4.9 33.2 1.0

Magnesium binding site 4 out of 123 in the The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2905 b:30.6 occ:1.00 N6 X:A1667 4.0 31.1 1.0 N7 X:A1667 4.0 31.5 1.0 O6 X:G1668 4.1 30.6 1.0 OP1 X:G1987 4.4 44.8 1.0 N7 X:G1668 4.5 31.0 1.0 C5 X:A1667 4.7 31.6 1.0 C6 X:A1667 4.7 31.4 1.0 C6 X:G1668 5.0 30.8 1.0

Magnesium binding site 5 out of 123 in the The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2906 b:43.0 occ:1.00 OP1 X:C1765 2.0 45.8 1.0 P X:C1765 3.5 46.9 1.0 OP1 X:A1777 3.6 46.7 1.0 OP2 X:A1777 3.9 46.3 1.0 O2' X:G1763 4.1 49.4 1.0 O5' X:C1765 4.3 46.9 1.0 P X:A1777 4.3 46.2 1.0 OP2 X:C1765 4.3 47.4 1.0 N3 X:G1763 4.3 49.0 1.0 O6 X:G1767 4.3 57.6 1.0 O3' X:A1764 4.5 54.0 1.0 N2 X:G1763 4.5 48.5 1.0 C5' X:C1765 4.7 46.7 1.0 OP2 X:U1766 4.7 48.0 1.0 C2' X:G1763 4.8 50.0 1.0 C1' X:G1763 4.9 49.4 1.0 C2 X:G1763 4.9 49.0 1.0 C5' X:A1777 4.9 47.7 1.0 N4 X:C1779 4.9 54.3 1.0

Magnesium binding site 6 out of 123 in the The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2907 b:49.7 occ:1.00 OP1 X:G844 3.3 53.0 1.0 N7 X:A956 3.9 60.3 1.0 C8 X:A956 4.1 61.2 1.0 OP2 X:G955 4.2 61.9 1.0 N1 X:A2427 4.5 52.7 1.0 P X:G844 4.5 53.2 1.0 OP1 X:G955 4.6 61.6 1.0 CG I:ARG40 4.6 50.2 1.0 OP1 X:U577 4.6 46.6 1.0 O3' X:G843 4.7 61.4 1.0 N6 X:A2427 4.8 51.5 1.0 P X:G955 4.9 62.3 1.0

Magnesium binding site 7 out of 123 in the The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2908 b:34.7 occ:1.00 OP2 X:A1693 2.4 48.3 1.0 P X:A1693 3.8 47.8 1.0 N7 X:A1693 4.0 48.4 1.0 C8 X:A1693 4.2 47.9 1.0 N7 X:A1694 4.2 47.0 1.0 O5' X:A1693 4.2 47.4 1.0 OP2 X:C1692 4.4 45.5 1.0 OP1 X:A1693 4.5 47.6 1.0 O3' X:C1692 4.9 43.2 1.0 N6 X:A1694 4.9 48.3 1.0 O5' X:C1692 4.9 44.6 1.0

Magnesium binding site 8 out of 123 in the The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2909 b:36.3 occ:1.00 OP2 X:C1340 1.9 36.0 1.0 P X:C1340 3.4 35.9 1.0 OP2 X:U1339 3.5 34.7 1.0 N7 X:G1337 3.6 36.6 1.0 O5' X:C1340 3.9 35.9 1.0 C8 X:G1337 4.0 36.1 1.0 N7 X:G1341 4.2 38.9 1.0 OP1 X:U1339 4.3 34.7 1.0 OP1 X:C1340 4.4 36.3 1.0 P X:U1339 4.4 34.4 1.0 O3' X:U1339 4.5 35.2 1.0 O6 X:G1341 4.5 38.0 1.0 C5 X:G1337 4.6 36.7 1.0 OP2 X:G1341 4.7 40.1 1.0 C3' X:U1339 4.9 34.6 1.0 C6 X:C1340 5.0 35.2 1.0

Magnesium binding site 9 out of 123 in the The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2910 b:34.8 occ:1.00 OP2 X:A1681 2.3 34.9 1.0 OP2 X:G1975 3.4 34.6 1.0 P X:A1681 3.8 35.1 1.0 N7 X:G1975 4.0 33.4 1.0 O6 X:G1684 4.0 36.1 1.0 N6 X:A1682 4.1 35.6 1.0 O6 X:G1683 4.2 35.6 1.0 N7 X:A1681 4.3 34.8 1.0 N7 X:A1682 4.4 36.3 1.0 O6 X:G1975 4.5 33.8 1.0 O5' X:A1681 4.6 35.5 1.0 C3' X:U1680 4.6 34.1 1.0 C2' X:U1680 4.6 33.8 1.0 OP1 X:A1681 4.6 35.6 1.0 P X:G1975 4.7 34.2 1.0 C5 X:G1975 4.7 33.5 1.0 O3' X:U1680 4.7 34.6 1.0 C6 X:G1684 4.8 36.2 1.0 C8 X:G1975 4.8 33.3 1.0 N7 X:G1683 4.8 36.8 1.0 C8 X:A1681 4.9 35.0 1.0 C6 X:G1975 4.9 33.6 1.0 C6 X:G1683 4.9 36.0 1.0

Magnesium binding site 10 out of 123 in the The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2911 b:46.4 occ:1.00 OP1 X:A815 2.0 47.6 1.0 P X:A815 3.4 48.5 1.0 OP2 X:G687 3.9 48.7 1.0 O4 X:U816 3.9 46.2 1.0 OP2 X:A688 4.1 53.3 1.0 O3' X:G814 4.2 55.6 1.0 OP2 X:A815 4.2 48.2 1.0 O5' X:A815 4.5 49.4 1.0 N6 X:A817 4.5 56.9 1.0 C4 X:U816 4.6 47.0 1.0 C5 X:U816 4.7 48.1 1.0 N7 X:A817 4.7 59.1 1.0 O5' X:A688 4.9 53.0 1.0 O5' X:G687 5.0 47.0 1.0 P X:G687 5.0 47.7 1.0

M.Krupkin, I.Wekselman, D.Matzov, Z.Eyal, Y.Diskin Posner, H.Rozenberg, E.Zimmerman, A.Bashan, A.Yonath. Avilamycin and Evernimicin Induce Structural Changes in Rproteins UL16 and Ctc That Enhance the Inhibition of A-Site Trna Binding. Proc.Natl.Acad.Sci.Usa V. 113 E6796 2016.
ISSN: ESSN 1091-6490
PubMed: 27791159
DOI: 10.1073/PNAS.1614297113